Epigenetic regulation of higher order chromatin conformations and networks

Higher order chromatin conformations result from the packaging of the genome into the physical confines of the cell nucleus. Structural hallmarks of the nucleus influence the spatio-temporal behavior of genome underlying the regulation of genomic functions. Moreover, accumulated data show that the physical proximities between interphase chromatin fibers significantly contribute to the regulation of genomic transcription, replication and repair. The dynamic patterns of spatial crosstalk between genomic regions are, moreover, controlled by environmental cues to fine-tune gene transcription.

The studies in this thesis focus on the nature of higher order chromatin conformations and networks and their developmental regulation in mouse and human model systems. The thesis also includes the description of a novel technique that enables the visualization of higher order chromatin proximities in single cells at a resolution far beyond that of the microscope.

Specifically, we identified developmentally regulated genome-wide chromosomal interactomes impinging on the H19 imprinting control region (ICR) in embryonic stem (ES) cells and derived embryoid bodies (EBs). The chromosomal interactomes appear poorly conserved between mouse and human. We further constructed chromosomal interaction networks with crosswise interacting pattern and present the modular topology of the human networks. The molecular glue connecting chromosomes to each other was identified as poly(ADP-ribose). TGFβ signaling was shown to rapidly rewire the chromosomal interaction networks by targeting a CTCF-PARP1 feed-back loop to decrease poly(ADP-ribose) levels in the nucleus.

We further captured a developmentally conserved imprinted interaction network, which is dependent on CTCF binding sites on the maternal H19 ICR allele. This network was shown to function as a vehicle to transfer epigenetic states from H19/Igf2 domain to other imprinted domains it interacts with. We propose the principle of non-allelic transvection of epigenetic states as a notable functional outcome of the physical contacts between chromatin fibers.

Finally, we invented Chromatin In Situ Proximity (ChrISP), which is a novel technique to identify and visualize proximities between chromatin fibers or between chromatin fiber as well as structural hallmarks in single cells at a high resolution. By employing the ChrISP technique we demonstrated that modification of epigenetic marks by environmental cues triggers large-scale changes in chromosome conformations.

It is concluded that higher order chromatin conformations and networks are epigenetically regulated by environmental cues and significantly contribute to the regulation of genomic functions during developmental and pathological processes.

List of scientific papers

I. Kuljeet Singh Sandhu, Chengxi Shi, Mikael Sjölinder, Zhihu Zhao, Anita Göndör, Liang Liu, Vijay K Tiwari, Sylvain Guibert, Lina Emilsson, Marta P Imreh, and Rolf Ohlsson (2009). Nonallelic transvection of multiple imprinted loci is organized by the H19 imprinting control region during germline development. Genes & Development. 23(22), 2598-­‐2603.
https://doi.org/10.1101/gad.552109

II. Anita Göndör, Alejandro Fernandez Woodbridge, Chengxi Shi, Erik Aurell, Marta P Imreh, and Rolf Ohlsson (2010). Window into the complexities of chromosome interactome. Cold Spring Harbor Symposia on Quantitative Biology. 75, 493-­‐500.
https://doi.org/10.1101/sqb.2010.75.049

III. Anita Göndör, Alejandro Fernandez Woodbridge, Noriyuki Sumida, Xingqi Chen, Samer Yammine, Moumita Biswas, Olga Loseva, Chengxi Shi, György Stuber, Balazs Nemeti, Maria Israelsson, Thomas Helleday, Marta P Imreh, and Rolf Ohlsson. TGFβ regulates physical interactions between chromosomes mediated by poly(ADP-­ribose). [Manuscript]

IV. Xingqi Chen, Chengxi Shi, Samer Yammine, Anita Göndör, Mariliis Tark-­Dame, Daniel Rönnlund, Alejandro Fernandez Woodbridge, Noriyuki Sumida, Jerker Widengren, Marta P Imreh, and Rolf Ohlsson. Single cell analysis reveals that H3K9 methylation organizes large, finger-­like chromatin hubs radially impinging on the nuclear membrane to protect against large-­scale reorganization of chromosome conformations. [Submitted]